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312d

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Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WATSON-CRICK BASE PAIR

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Retrieved from "http://52.214.119.220/wiki/index.php/312d"

Categories: Large Structures | Eichman BF | Ho PS | Mooers BHM

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-[[Image:312d.gif|left|200px]]<br /><applet load="312d" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="312d, resolution 1.800&Aring;" />
-'''Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WATSON-CRICK BASE PAIR'''<br />
-==Overview==
+==Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WATSON-CRICK BASE PAIR==
-We have solved the structures of the homoduplex d(Gm5CGCGCG)2, and the, heteroduplexes d(GCGCGCG)/d(TCGCGCG) and d(GCGCGCG)/d(CCGCGCG). The, structures form six base-pairs of identical Z-DNA duplexes with single, nucleotides overhanging at the 5'-ends. The overhanging nucleotide from, one strand remains stacked and sandwiched between the blunt-ends of two, adjacent Z-DNA duplexes, while the overhanging base of the opposing strand, is extra-helical. The stacked and the extra-helical bases from adjacent, duplexes pair to form a distorted d(G x G) reverse Hoogsteen base-pair in, the d(Gm5CGCGCG)2 homoduplex, and d(G x T) reverse wobble and d(G x C), reverse Watson-Crick base-pairs in the d(GCGCGCG)/d(TCGCGCG) and, d(GCGCGCG)/d(CCGCGCG) heteroduplexes, respectively. Interestingly, only, the d(G,T) and d(G x C) base-pairs were observed in the heteroduplexes, suggesting that both the d(G x T) reverse wobble and d(G x C) reverse, Watson-Crick base-pairs are more stable in this crystal environment than, the d(G x G) reverse Hoogsteen base-pair. To estimate the relative, stability of the three types of reverse base-pairs, crystals were grown, using various mixtures of sequences and their strand compositions analyzed, by mass spectrometry. The d(G x C) reverse Watson-Crick base-pair was, estimated to be more stable by approximately 1.5 kcal/mol and the d(G x T), reverse wobble base-pair more stable by approximately 0.5 kcal/mol than, the d(G x G) reverse Hoogsteen base-pair. The step during crystallization, responsible for discriminating between the strands in the crystal is, highly cooperative, suggesting that it occurs during the initial, nucleating event of crystal growth.
+<StructureSection load='312d' size='340' side='right'caption='[[312d]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[312d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=312D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=312D FirstGlance]. <br>
-D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=NCO:'>NCO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=312D OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=312d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=312d OCA], [https://pdbe.org/312d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=312d RCSB], [https://www.ebi.ac.uk/pdbsum/312d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=312d ProSAT]</span></td></tr>
-The structures and relative stabilities of d(G x G) reverse Hoogsteen, d(G x T) reverse wobble, and d(G x C) reverse Watson-Crick base-pairs in DNA crystals., Mooers BH, Eichman BF, Ho PS, J Mol Biol. 1997 Jun 27;269(5):796-810. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9223642 9223642]
+</table>
-[[Category: Protein complex]]
+__TOC__
-[[Category: Eichman, B.F.]]
+</StructureSection>
-[[Category: Ho, P.S.]]
+[[Category: Large Structures]]
-[[Category: Mooers, B.H.M.]]
+[[Category: Eichman BF]]
-[[Category: MG]]
+[[Category: Ho PS]]
-[[Category: NCO]]
+[[Category: Mooers BHM]]
-[[Category: double helix]]
-[[Category: flipped-out base]]
-[[Category: overhanging base]]
-[[Category: z-dna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 21:34:47 2008''

312d

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Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WATSON-CRICK BASE PAIR

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